Nanonews: proposal on new sequencing technique

Our very own Biophysics and Physics 2 teacher Chirlmin Joo received a VICI grant in April this year. This is awarded to him for his proposal on a new technique that allows researchers to sequence one protein at a time. The method makes use of probing the protein profile.

Proteins perform most of the functions in living cells, forming the basis for life. To understand biological processes, including diseases, it is critical to monitor the protein composition of cells by identifying each protein species. This can be done by sequencing; however, in practice protein sequencing remains an enormous challenge. Joo proposed to develop a novel single-molecule protein sequencing technique, which will overcome the challenges of the existing methods.

This novel sequencing technique is based on a new single-molecule method, FRET X. It is an advanced version of the widely used method single-molecule FRET. This is the technique in which a protein is tagged with different fluorophores, where one of the two is excited using fluorescent microscopy. This excited fluorophore emits light at such a wavelength that the other fluorophore becomes excited and emits light at its own specific wavelength. This can be very helpful to study protein dynamics. However, in order to study the structure of biomolecules, a new approach is needed.

This is exactly what Chirlmin Joo Lab set out to do. In his proposal, Joo described a technique in which proteins are labeled with multiple short DNA strands which are in turn bound to fluorophores. By sequentially exchanging the DNA strands, the distance between each pair can be measured very precisely, which tells us something about the structure of the protein of interest.

What makes this technique so revolutionary is its accuracy. Using FRET X, researchers can probe a single protein many times, to increase the accuracy of its structural measurements. This makes that this technique generates ultrahigh-resolution data. By comparing these results to protein databases, researchers will be able to make accurate predictions about a protein’s amino acid sequence.

As the Chirlmin Joo Lab is part of Bionanoscience at TU Delft, it is open for BEP students. Who knows, maybe in some time you can experience working with this technique yourself! Joo’s proposal can be found using the reference below.

In case you are very excited to read more about Joo’s proposal, its reference can be found using below.

  1. Filius, S. Kim, I. Severins & C. Joo, 2021. ‘High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)’, Nano Letters 2021,  21 (7), 3295-3301


Taken from mRNA edition 3, year 2020-2021. Text by Sten de Schrijver